Sequence
atgc intronic sequence ATGC exonic sequencegtaggtatactttgtctttatattccatctaatggcttcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21180.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g08018.1 (Oryza sativa), 3'ss of exon 6
gtaggtatactttg-tctttatattcc-atctaa--tggcttcagagttaaatgactatatggccttatt-tattgttgtattca---tatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
||| | || | || | |||| || | | | ||| | | || | | || |||| | | || || | |||||||| || ||||| || | ||||||||||||||||||| ||||||||||| || ||||| || |||||||||||
gtaagattatgtaaatccatgcattctgatttgatttatgttctatgctgtttgtatttctgagattataatgaaactaaatacaccttttagGTCCCGGCTGATGGTGTTTTGGTTAGTGGTCATTCTCTTGCCATTGATGAATCCAGTATGACTGGGGAAAGCAAGATC
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 10
-------------gtaggtatactttgtctttatattccatctaatggcttcagagttaaatgactatat--ggccttatttattgt-tgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
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aacatgtgctgtggtgggaaaaattgattttagtgtttaaccaaacaagcactga-ctagttttctatattctatgtgaactactctatggatgctctcagGTTCCTGCCGATGGAGTTGTAATCACTGGTCACTCTCTTGCCATTGATGAATCGAGTATGACTGGTGAAAGCAAGATT
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 9
--------------------gtaggtatactttgtctttatattccatctaatggcttcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
|| || | || | || | || | | || | || || | |||| || || | ||| | ||| ||| ||| ||||| |||||||| |||| | |||||| || ||||| ||||||||||| || ||||| |||||||||||||||
acatttgaacatgtgctgtggtgggagaaattgattttagtgtttaaccaaacaaggactga-ctagttttctatgtgaactactatatggatgttctca----gGTTCCTGCTGATGGAGTTGTAATCACTGGTCACTCGCTTGCCATTGATGAATCGAGTATGACTGGTGAAAGCAAGATT
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 11
gtaggtatactttgtctttatattccatctaatggcttcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
|| || | | | ||| | | ||| | |||| | | | | | | ||| | || | ||||| ||||| |||||||| |||| | || ||||| ||||| ||||||||||| || ||||| |||||||||||||||
gtgagtttgtatggcattttgagtttgtctgtaaattgagcagttttctttgttcaccgattactctatgggcatact----tagGTTCCTGCTGATGGAGTATTAATCACGGGCCATTCACTTGCAATTGATGAATCCAGTATGACTGGTGAAAGCAAGATT
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 11
gtaggtatactttgtctttatattccatctaatggcttcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
|| || | | || ||| | | ||| | ||| | | | | | | ||| | || ||| ||| ||||| |||||||| |||| | || ||||| ||||| ||||||||||| || ||||| |||||||||||||||
gtgagtttgtatggtattttgagtttgtctggaaattgagcagtattttttgttcaccgattactctatgggcatactca----gGTTCCTGCTGATGGAGTATTAATCACGGGCCATTCACTTGCAATTGATGAATCCAGTATGACTGGTGAAAGCAAGATT
upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 10
gtaggtatactttgtcttt---atattccatctaatggct----tcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
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gtaagtgtacttcgattgctgaatattgtcttgaatacctctatttattttaaaattaactcgagtcaccgcgttttggtgt-tttatccagGTCCCTGCAGATGGAATCTTAATTACTGGTCATTCTCTTGCAATTGATGAATCTAGCATGACTGGTGAAAGCAAGATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatggcttcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
atctaat putative branch site (score: 3)
ttatttattgttgtat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtatactttgtctttatattccatctaatggcttcagagttaaatgactatatggccttatttattgttgtattcatatagGTCCCTGCGGATGGAGTGCTAATTAGTGGTCATTCTCTTGCTATTGATGAATCTAGCATGACCGGTGAAAGCAAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA